GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Pseudomonas stutzeri RCH2

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate GFF2541 Psest_2591 3-isopropylmalate dehydratase, large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__psRCH2:GFF2541
          Length = 475

 Score =  607 bits (1564), Expect = e-178
 Identities = 308/470 (65%), Positives = 366/470 (77%), Gaps = 8/470 (1%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           KTLY+KL++ H V   ++ + L+YIDRH++HEVTSPQAF+GLR   R   +     AT D
Sbjct: 4   KTLYDKLWEMHEVKRRDDGSSLIYIDRHILHEVTSPQAFEGLRLANRKPWRIDANIATPD 63

Query: 63  HNVSTQTKDINACG------EMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQG 116
           HNV T TK     G      E++RIQ+Q L +NC +FG+  + +N   QGIVHV+GPEQG
Sbjct: 64  HNVPT-TKGERQGGLEAIADEVSRIQVQTLDENCDDFGILEFKMNDVRQGIVHVIGPEQG 122

Query: 117 VTLPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAP 176
            TLPGMT+VCGDSHT+THGAFGALA GIGTSEVEHVLATQ L   + K M++ V+GK   
Sbjct: 123 ATLPGMTVVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQCLVAKKMKNMQVRVEGKLPF 182

Query: 177 GITAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPD 236
           G+TAKDIVLA+IGK G+AGG GH +EF G AIRDLSMEGRMT+CNM+IE GA+ G+VA D
Sbjct: 183 GVTAKDIVLAVIGKIGTAGGNGHALEFAGSAIRDLSMEGRMTICNMSIEAGARVGMVAVD 242

Query: 237 ETTFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQ 296
           E T  YV+GR  APKG D+D AV  W+ L +D+ A FDTVV L+AE+I PQV+WGT+P  
Sbjct: 243 EKTIAYVEGRPFAPKGDDWDKAVELWQGLVSDDDAVFDTVVELKAEDIKPQVSWGTSPEM 302

Query: 297 VISVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLR 356
           V++V+  +PDPA  ADPV+R S  +AL YMGL    P+TE+ +D+VFIGSCTNSRIEDLR
Sbjct: 303 VLAVDQKVPDPAVEADPVKRDSIMRALKYMGLNANQPITEIKLDRVFIGSCTNSRIEDLR 362

Query: 357 AAAEIAKGRKVAPGV-QALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNN 415
           AAAE+AKGRKVA  V QALVVPGSG VK QAEAEGLDKIF+EAGFEWR PGCSMCLAMN 
Sbjct: 363 AAAEVAKGRKVAANVKQALVVPGSGLVKQQAEAEGLDKIFVEAGFEWREPGCSMCLAMNP 422

Query: 416 DRLNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
           D+L  GE CASTSNRNFEGRQG GGRTHLVSPAMAAAAAVTGHF D+R +
Sbjct: 423 DKLGSGEHCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAVTGHFIDVREL 472


Lambda     K      H
   0.317    0.134    0.396 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 758
Number of extensions: 20
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 466
Length of database: 475
Length adjustment: 33
Effective length of query: 433
Effective length of database: 442
Effective search space:   191386
Effective search space used:   191386
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate GFF2541 Psest_2591 (3-isopropylmalate dehydratase, large subunit)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

Software error:

../bin/blast/fastacmd -i /tmp/list.14523.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.14523.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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